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Livingston was born in Dallas, Texas and grew up in Los Angeles, where she attended Beverly Hills High School. She graduated from Yale University in 1983, where she studied photography, drawing, and painting with a minor in English Literature. Livingston is the niece of the late film director Alan J. Pakula, who initially warned her away from film directing, but later proved encouraging. She lives in Brooklyn, New York.

Livingston's documentary about a New York gay and transgender Black and Latino ball culture won the 1991 Sundance Grand Jury Prize and was a key film both in the emerging American independent film movement and in the nascent New Queer Cinema. Paris is Burning was one of Miramax Films' earliest successes, and helped pave the way for a current crop of commercially successful documentary films. It was one of the best films of 1991 according to The Los Angeles Times, Time Magazine, The Washington Post, and NPR; New York Magazine, in its 2008 40th anniversary edition, called it one of the most influential cultural works to come out of New York City in 40 years.

Several of the most heavily featured performers wished to sue in 1991 for a share of the film's profits. Paris DuPree sought the largest settlement with $40 million for unauthorized use of her ball. Dupree and others said they were deceived about the film's purpose and wanted compensation. The producers stated that they had always planned on compensating the principal participants. All dropped their claims after their attorneys confirmed that they had signed releases. The producers then distributed approximately $55,000 among thirteen of the participants.

Two of Livingston's short films, Hotheads and Who's the Top?, explore queer topics. Hotheads, a 1993 documentary created through the AIDS research-friendly Red Hot Organization, explores two comedians' responses to violence against women: cartoonist Diane Dimassa, and writer/performer Reno. Hotheads was shown on MTV and KQED and released on Polygram Video as part of Red Hot's No Alternative compilation.

Who's the Top?, Livingston's first dramatic film, a 22-minute-long short film, premiered at Berlin International Film Festival in 2005, and stars Marin Hinkle, Shelly Mars, and Steve Buscemi. The film, a lesbian sex comedy with musical numbers, also features 24 Broadway dancers choreographed by Broadway choreographer John Carrafa in the manner of Busby Berkeley. The film screened at over 150 film festivals on nearly every continent, including theatrical runs at Boston's Museum of Fine Arts and London's Institute of Contemporary Arts.

Through the Ice is a digital short, commissioned in 2005 for public television station WNET-New York, about the accidental drowning of Miguel Flores in Prospect Park, Brooklyn; the film was also seen at the 2006 Sundance Film Festival.

Livingston is currently directing a documentary feature, Earth Camp One, a first person narrative about grief, loss, and a hippie summer camp in the 1970s, also a broader essay on social and cultural attitudes about death and impermanence, was begun on a 2000 Guggenheim fellowship and was also partially funded by Netflix. She is also developing Prenzlauer Berg, an ensemble film set in the art worlds of New York and East Berlin in the late 80s. She has appeared in others' films, speaking about film and filmmaking, including Fabulous! The Story of Queer Film, created for the cable channel IFC Television in 2006.

In 2011, Livingston directed a video for Elton John's show at Caesar's Palace in Las Vegas; the piece is a series of black and white moving-image portraits of a variety of New Yorkers that accompanies the song Mona Lisas and Mad Hatters. The show will run through 2015.

Livingston has taught film at Yale, Brooklyn College, and Connecticut College, and lectured at dozens of colleges and cultural institutions in the US, including Williams College and Rutgers College Writers House; and at several institutions abroad, including the South Africa School of Motion Picture Medium and Live Performance (AFDA), Johannesburg; and the Hochschule für Film und Fersehen (Munich). Fellowships have included the Guggenheim Foundation, the Getty Center, the German Academic Exchange (DAAD), The MacDowell Colony, and the National Endowment for the Arts (NEA.)